My name is Gilbert Permalloo. I am a Research Project Officer and I am presently working on roots architecture and rhizosphere of wheat. I worked in sugarcane agronomy for about 24 years and I was doing a little bit of basic programming in Fortran 77 and GWBasic about 30 years ago. Most of my data manipulation and visualisation are done in Excel. I could not write any code in R before I joined Data School and I was spending lots of time working with data in spreadsheets. On the otherhand, I am amazed to witness every day the marvel that R can do with data manipulation and visualisation.
The aim of this project is to investigate the use of portable X-Ray fluorescense spectrocopy (pXRF) as a rapid method to quantify the amount of phosphorus accumulated in straw and grains (Photo-1 shows pXRF used). About 200 grab samples were taken from one of three trials at 0kg and 30kg of phosphorus per hectare as treatments for this study. The straw and grains were ground (Photo-2), and scanned by the pXRF. Two large datasets were generated by the pXRF; the chemistry dataset is composed of a wide range of chemical elemental composition quantified in ppm, whereas the beamspectra, are spectral values from three X-ray beams. R has been used to clean, tidy and re-organised the data, as well as for graphical visualisation. Data for phosphorus have been extracted from the large pXRF generated-dataset and merged with a dataframe that contains unique identification numbers (SampleID) that links the data to the sample source (STEM_ID) and other spreadsheets that contain agronomical data for each sample.
Figures 1 and 2 show a relatively higher amount of phosphorus detected in the grains as compared to the straw. A slightly higher correlation between straw and grains for phosphorus assimilated under the 30kg/ha P treatment in comparison to the 0kg/ha P. Figure 2 shows that the level of P detected in the straw does not correlate with the grain yield. However, the amount of phosphorus detected in grains for the two treatments correlate differently to yield. Grains produced under the low treatment tend to show a slight positive correlation to yield as opposed to the 30kg/ha treatment, which has a negative correlation to yield.
Photo-1: pXRF instrument used to quantify amount of phosphorus in straw and grains
Photo-2: Ground grains, empty cup and ground grains packed in cup